I've been meaning to get LUFA running on my xplain. But getting xmegaduino ported to the spark fun breakout has taken priority.
You probably need a more recent avr-gcc. I'm guessing it can't compile for the xmega, though when I've seen that it usually gives an error message rather than crashing. Easiest thing to do is download the whole package for windows.
If you still have problems, can you run "sh -x run.sh" from the windows build folder? Attach the output.
I suspect it will break while compiling the bootloader, I think that's the only thing we run avr-gcc on when building. If so, cd to hardware/xmegaduino/bootloaders/xplain and run "make". Attach the output.